Joe Pendleton (Robert Montgomery) is a fast-rising boxer, preparing for a big title match with champion Ralph Murdock. To the displeasure of his manager, Max Corkle (James Gleason), Joe flies his own small plane to New York for the match. As he flies, playing his "lucky" saxophone in the aircraft, a cable snaps and the plane plummets to earth.

Joe is next seen walking in the clouds with "Messenger 7013" (Edward Everett Horton) being processed for his journey to heaven. However, the Messenger, new to his job, had mistakenly taken Joe an instant before the crash, a violation of heavenly protocol, so the Messenger's boss, Mr. Jordan (Claude Rains) rules that he is entitled to return to Earth. His body has, in the meantime, been cremated, so he must select another body from someone who is about to die.

After much searching the Earth with Mr. Jordan, Joe settles on the body of Bruce Farnsworth, a millionaire industrialist who has just been murdered by his wife, Julia (Rita Johnson) and her boyfriend, Tony (John Emery). As he settles in to his new role, his first act to rectify a crooked stock deal that Farnsworth had accomplished and to exonerate the man who had been framed for it, much to the consternation of Farnsworth's company board of directors. The freed man's daughter, Betty Logan (Evelyn Keyes), is surprised but very grateful, and she and Joe/Farnsworth are attracted to each other.

Joe is still obsessed with becoming a boxing champion so he decides that, in the body of Farnsworth, he will train to do just that. He calls in his old manager, Max, who is ultimately convinced that it is really Joe, as he knows facts that only his former boxer could. However, Mr. Jordan arrives to tell Joe that he will again have to find a new body, as Farnsworth is about to be murdered, this time successfully, by his wife and her boyfriend.

As the murder is being investigated by the police in the Farnsworth mansion, Max turns on the radio to listen to the boxing title match, being fought between Murdock and Lou Gilbert. The announcer says that Murdock has gone to the floor without the punch being seen. Mr. Jordan explains to Joe, that Murdock was shot by gamblers. Joe realizes that this is his opportunity to become a boxing champ, and he is instantly transported to the boxing ring, where he inhabits the fallen body of Murdock. He rises from the floor and delivers the knockout punch to Gilbert.

Mr. Jordan erases Joe's memories of all that has happened, so he only now knows himself as Murdock. As he leaves his dressing room, he encounters Betty Logan. They chat and, each experiencing a sense of strange familiarity with the other, they agree to go have coffee together.

Here Comes Mr. Jordan was from a play," Heaven Can Wait", by Harry Seagall, and was remade as Heaven Can Wait in 1978, and as Down to Earth with Chris Rock in 2001. The latter title was used as a semi-sequel, the musical Down to Earth, 1947, with Rita Hayworth. In India, Here Comes Mr. Jordan was remade as Jhuk Gaya Aasman (1968).